Wackerman started his musical career as a teen with a group called Bad4Good in 1991. Under Steve Vai's guidance, the band released one album in 1992 called Refugee, produced by Vai himself. However, the band disbanded shortly after. From 1993 to 2000, Wackerman was a member of Infectious Grooves, playing drums on the albums Groove Family Cyco in 1994 and Mas Borracho in 2000 as well as touring with the band. Shortly after his departure, he performed drums for the 2000 Vandals' album Look What I Almost Stepped In....

In 2006, for The Pick of Destiny tour, Wackerman was selected to feature as the Drummer for Tenacious D due to his previous work on the Vandals' Look What I Almost Stepped In... album, which both Jack Black and Kyle Gass cameo on. He would go on to play for Tenacious D at various festivals as well as support act and benefit concerts throughout 2008 to 2011. in 2012, Wackerman played with Tenacious D again on their Rize of the Fenix tour where he got the nickname "Thunderskin" from Jack Black for comical remark, making appearances on the Late Show with David Letterman, Late Night with Jimmy Fallon, The Tonight Show with Jay Leno and The Daily Show with Jon Stewart. They also performed at the 2012 Rock am Ring Festival. Wackerman also appeared in the music videos for their songs "Roadie" and "Rize of the Fenix". He would perform on their 2012 EP Tenacious D Jazz and their 2015 live album Tenacious D Live.

Wackerman formerly fronted Kidneys alongside fellow Tenacious D band member John Spiker. Initially, his brother, John Wackerman played with Kidneys, but he would later be replaced by Todd Hennig (Death By Stereo). A full-length self-titled album was released in 2007, and another album in 2012, entitled Hold Your Fire, is available for digital download. The band split ways in 2012.

Alongside Terry Bozzio, Wackerman contributed drums and percussion for Korn's untitled album. He is the frontman for Hot Potty. Wackerman is also the Drummer for the Innocent, a thrash metal band featuring Bassist Ryan Sinn (formerly of Angels & Airwaves and the Distillers), vocalist Brandan Schieppati (Bleeding Through), and Guitarist Dave Nassie (No Use for a Name). In March 2008, Wackerman joined Korn Guitarist James "Munky" Shaffer's newest solo project, experimental industrial rock band Fear and the Nervous System, alongside vocalist Steve Krolikowski (Repeater), Billy Gould (Faith No More), Leopold Ross (Error), and Zac Baird (Korn, Billy Goat). Brooks also played drums for Avril Lavigne. Brooks filled in for Travis Barker during Blink-182's 2013 tour of Australia in the Soundwave festival as well as their sideshows. Brooks was hired to record drums on former Blink-182 member Tom DeLonge's debut solo album To The Stars, appearing on the track "New World".

On November 4, 2015, it was revealed that Wackerman was the new Drummer for Avenged Sevenfold. Brooks was working with the band one year prior to the official announcement, because the band wanted to "fit in" with the new Drummer. Like the previous Drummer Arin Ilejay, but unlike the rest of the band members, he currently does not have a stage name. His first full-length album with the band was their October 2016 release The Stage, which showcased his progressive style of drumming, often using fast double-bass kicks and blast beats.